health-data-standards 3.4.3 → 3.4.4

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 53466a80b522c4dcf83771208231673cc56851c0
-  data.tar.gz: 54aa385a7bbd8d9bda56ed972ebf46d7c334c172
+  metadata.gz: a480121f52dadad4ea76ab611bfa5547873266df
+  data.tar.gz: 2a1f0fe2ae72b74f35d8db365da80e3d0654a915
 SHA512:
-  metadata.gz: 90331c3fa00028a7dd815255025dde27038255869afa26824ffdddedc2788c7784374d45bd7f8a5f211498a605a5c472e484e2fcd4e90bbdea0f557b84338651
-  data.tar.gz: 591bc0155567836813255795511fcdb4a5f6d373bf8b497960aec02503e2c91d7b3db969c29e08483a8f7acd4d1607e71bcdd1a3707f018398a6b5de2073ad59
+  metadata.gz: 37ef1885436c68bfeff5e2ea0b055365d6bc4ae4623c152cf0299646369a80a197bd8a3b89096f7c225ccbe049de2ffc1ac1e2da9aa741a88c6640231db6ef67
+  data.tar.gz: b54ff8e18fd0f0c47e54b6a2d46440d10307ef5965026b948972d4198fe54e6e3938e0c68b63e8d23a087cd19af8976a6aa7bb24a6bf8ca225fd438cc233f841

data/README.md

@@ -25,7 +25,14 @@ Please try to follow the [GitHub Coding Style Guides](https://github.com/stylegu
 Change Log
 ==========
 
+3.4.4
+
+* Updating the Measure model to deal with continuous variable and NQF and CMS ids through Measure.categories
+* Bug fix - Filters were not properly handled by the QueryCache
+* Bug fix - Fixed the order of populations in HQMF::PopulationCriteria::ALL_POPULATION_CODES so that DENEX is after denominator
+
 3.4.3 - March 6, 2014
+
 * Implemented support for providers in QRDA Cat III documents
 * Now handles null value HQMF expression value types
 

data/lib/health-data-standards/export/helper/html_view_helper.rb

@@ -19,6 +19,20 @@ module HealthDataStandards
             status
           end
         end
+
+        def decode_hqmf_description(description, oid)
+          if oid
+            definition = HealthDataStandards::Util::HQMFTemplateHelper.definition_for_template_id(oid)['definition']
+            status = HealthDataStandards::Util::HQMFTemplateHelper.definition_for_template_id(oid)['status']
+            unless status.blank?
+              "#{definition.titleize}, #{status.titleize}".to_sym  
+            else
+              "#{definition.titleize}".to_sym
+            end
+          else
+            description
+          end
+        end
       end
     end
   end

data/lib/health-data-standards/import/bundle/importer.rb

@@ -2,13 +2,13 @@ require 'zip/zipfilesystem'
 module HealthDataStandards
   module Import
     module Bundle
-      
+
       class Importer
 
-        SOURCE_ROOTS = {bundle: 'bundle.json', 
-                        libraries: File.join('library_functions','*.js'), 
-                        measures: 'measures', results: 'results', 
-                        valuesets: File.join('value_sets','json','*.json'), 
+        SOURCE_ROOTS = {bundle: 'bundle.json',
+                        libraries: File.join('library_functions','*.js'),
+                        measures: 'measures', results: 'results',
+                        valuesets: File.join('value_sets','json','*.json'),
                         patients: 'patients'}
         COLLECTION_NAMES = ["bundles", "records", "measures", "selected_measures", "patient_cache", "query_cache", "system.js"]
         CLEAR_ONLY_COLLECTIONS = ["system.js"]
@@ -36,19 +36,19 @@ module HealthDataStandards
               raise "A bundle with version #{bundle.version} already exists in the database. "
             end
 
-            HealthDataStandards::CQM::Bundle.where({:version => bundle.version}).each do |b| 
+            HealthDataStandards::CQM::Bundle.where({:version => bundle.version}).each do |b|
               puts "deleting existing bundle version: #{b.version}"
               b.delete
             end if options[:delete_existing]
 
             #find the highest bundle version and see if one is installed that is greater than the one
-            # we are currently installing.  Do not load the libs other wise 
+            # we are currently installing.  Do not load the libs other wise
             vers = bundle_versions.values.sort.reverse[0]
             if (vers.nil? || vers <= bundle.version || options["force_js_install"])
-              unpack_and_store_system_js(zip_file) 
+              unpack_and_store_system_js(zip_file)
             else
               puts "javascript libraries will not being updated as a more recent bundle version is already installed"
-            end  
+            end
             # Store the bundle metadata.
             unless bundle.save
               raise bundle.errors.full_messages.join(",")
@@ -56,9 +56,9 @@ module HealthDataStandards
             puts "bundle metadata unpacked..."
 
             measure_ids = unpack_and_store_measures(zip_file, options[:type], bundle, options[:update_measures])
-            unpack_and_store_patients(zip_file, options[:type], bundle)
+            unpack_and_store_patients(zip_file, options[:type], bundle) unless options[:exclude_results]
             unpack_and_store_valuesets(zip_file, bundle)
-            unpack_and_store_results(zip_file, options[:type], measure_ids, bundle)
+            unpack_and_store_results(zip_file, options[:type], measure_ids, bundle) unless options[:exclude_results]
 
           end
 
@@ -163,7 +163,7 @@ module HealthDataStandards
               contents.select! {|entry| measure_ids.include? entry['value']['measure_id']} if collection == 'patient_cache'
             end
 
-            contents.each do |document| 
+            contents.each do |document|
               if name == "by_patient"
                 # Set the patient_id to the actual _id of
                 # newly created patient record

data/lib/health-data-standards/models/cqm/measure.rb

@@ -19,7 +19,7 @@ module HealthDataStandards
       field :type, type: String
       field :category, type: String
       field :population_ids , type: Hash
-      field :oids, type: Array 
+      field :oids, type: Array
 
       field :population_criteria, type: Hash
       field :data_criteria, type: Array, default: []
@@ -39,29 +39,35 @@ module HealthDataStandards
       index sub_id: 1
       index _id: 1, sub_id: 1
       index bundle_id: 1
-      
+
       validates_presence_of :id
       validates_presence_of :name
 
       def self.categories
         pipeline = []
-        pipeline << {'$group' => {_id: "$id", 
+        pipeline << {'$group' => {_id: "$id",
                                   name: {"$first" => "$name"},
                                   description: {"$first" => "$description"},
-                                  sub_ids: {'$push' => "$sub_id"},
                                   subs: {'$push' => {"sub_id" => "$sub_id", "short_subtitle" => "$short_subtitle"}},
+                                  sub_ids: {'$push' => "$sub_id"},
+                                  nqf_id: {"$first" => "$nqf_id"},
+                                  cms_id: {"$first" => "$cms_id"},
+                                  continuous_variable: {"$first" => "$continuous_variable"},
                                   category: {'$first' => "$category"}}}
 
         pipeline << {'$group' => {_id: "$category",
-                                  measures: {'$push' => {"id" => "$_id", 
+                                  measures: {'$push' => {"id" => "$_id",
                                              'name' => "$name",
                                              'description' => "$description",
                                              'subs' => "$subs",
-                                             'sub_ids' => "$sub_ids"
+                                             'sub_ids' => "$sub_ids",
+                                             'nqf_id' => "$nqf_id",
+                                             'cms_id' => "$cms_id",
+                                             'continuous_variable' => "$continuous_variable"
                                             }}}}
 
         pipeline << {'$project' => {'category' => '$_id', 'measures' => 1, '_id' => 0}}
-  
+
         pipeline << {'$sort' => {"category" => 1}}
         Mongoid.default_session.command(aggregate: 'measures', pipeline: pipeline)['result']
       end
@@ -76,7 +82,7 @@ module HealthDataStandards
       def key
         "#{self['id']}#{sub_id}"
       end
-      
+
       def is_cv?
         ! population_ids[MSRPOPL].nil?
       end
@@ -84,7 +90,7 @@ module HealthDataStandards
       def self.installed
         Measure.order_by([["id", :asc],["sub_id", :asc]]).to_a
       end
-      
+
 
       # Finds all measures and groups the sub measures
       # @return Array - This returns an Array of Hashes. Each Hash will represent a top level measure with an ID, name, and category.
@@ -94,14 +100,14 @@ module HealthDataStandards
                     if (obj.sub_id != null)
                       prev.subs.push({id : obj.id + obj.sub_id, name : obj.subtitle});
                   }'
-        
+
         self.moped_session.command( :group=> {:ns=>"measures", :key => {:id=>1, :name=>1, :category=>1}, :initial => {:subs => []}, "$reduce" => reduce})["retval"]
       end
 
       def display_name
         "#{self['cms_id']}/#{self['nqf_id']} - #{name}"
       end
-      
+
 
       def set_id
         self.hqmf_set_id

data/lib/health-data-standards/models/cqm/query_cache.rb

@@ -5,7 +5,7 @@ module HealthDataStandards
       include Mongoid::Timestamps
       store_in collection: 'query_cache'
 
-      field :calculation_date, type: Time 
+      field :calculation_date, type: Time
       field :status, type: Hash
       field :measure_id, type: String
       field :sub_id, type: String
@@ -21,8 +21,13 @@ module HealthDataStandards
       field :OBSERV, type: Float
       field :supplemental_data, type: Hash
 
-      def self.aggregate_measure(measure_id, effective_date, filter=nil, test_id=nil)
-        cache_entries = self.where(effective_date: effective_date, measure_id: measure_id, test_id: test_id, filter: filter)
+      def self.aggregate_measure(measure_id, effective_date, filters=nil, test_id=nil)
+        query_hash = {'effective_date' => effective_date, 'measure_id' => measure_id,
+                      'test_id' => test_id}
+        if filters
+          query_hash.merge!(filters)
+        end
+        cache_entries = self.where(query_hash)
         aggregate_count = AggregateCount.new(measure_id)
         cache_entries.each do |cache_entry|
           aggregate_count.add_entry(cache_entry)
@@ -38,7 +43,7 @@ module HealthDataStandards
         population_ids.has_key?('MSRPOPL')
       end
 
-      
+
     end
   end
 end

data/lib/health-data-standards/tasks/bundle.rake

@@ -22,7 +22,7 @@ namespace :bundle do
 
 
   desc 'List bundles'
-  task :list  => [:environment] do 
+  task :list  => [:environment] do
      Bundle.where({}).each do |b|
       puts "Bundle #{b.title} - #{b.version}  active: #{b.active}"
      end
@@ -30,14 +30,15 @@ namespace :bundle do
 
 
   desc 'Import a quality bundle into the database.'
-  task :import, [:bundle_path,  :delete_existing,  :update_measures, :type, :create_indexes] => [:environment] do |task, args|
+  task :import, [:bundle_path,  :delete_existing,  :update_measures, :type, :create_indexes, :exclude_results] => [:environment] do |task, args|
     raise "The path to the measures zip file must be specified" unless args.bundle_path
     options = {:delete_existing => (args.delete_existing == "true"),
     					 :type => args.type,
-    					 :update_measures => (args.update_measures == "true")
+    					 :update_measures => (args.update_measures == "true"),
+               :exclude_results => (args.exclude_results == "true")
     					}
 
-    bundle = File.open(args.bundle_path)    
+    bundle = File.open(args.bundle_path)
     importer = HealthDataStandards::Import::Bundle::Importer
     bundle_contents = importer.import(bundle, options)
 
@@ -52,30 +53,30 @@ namespace :bundle do
     end
 
     puts "Successfully imported bundle at: #{args.bundle_path}"
-    puts "\t Imported into environment: #{Rails.env.upcase}" if defined? Rails 
+    puts "\t Imported into environment: #{Rails.env.upcase}" if defined? Rails
     puts "\t Loaded #{args.type || 'all'} measures"
     puts "\t Sub-Measures Loaded: #{counts[:measures]}"
     puts "\t Test Patients Loaded: #{counts[:records]}"
     puts "\t Extensions Loaded: #{counts[:extensions]}"
     puts "\t Value Sets Loaded: #{counts[:value_sets]}"
-    
+
 
   end
-  
+
   # this task is most likely temporary.  Once Bonnie can handle both EP and EH measures together, this would no longer be required.
   desc 'Merge two bundles into one.'
   task :merge, [:bundle_one,:bundle_two] do |t, args|
     raise "Two bundle zip file paths to be merged must be specified" unless args.bundle_one && args.bundle_two
-    
+
     tmpdir = Dir.mktmpdir
     ['measures','patients','library_functions','results', 'sources', 'value_sets'].each do |dir|
-      
+
       FileUtils.mkdir_p(File.join(tmpdir, 'output', dir))
-      
+
     end
-      
+
     begin
-      
+
       ({'one'=>args.bundle_one,'two'=>args.bundle_two}).each do |key, source|
         Zip::ZipFile.open(source) do |zip_file|
           zip_file.each do |f|
@@ -85,8 +86,8 @@ namespace :bundle do
           end
         end
       end
-      
-      
+
+
       ['measures','patients','library_functions', 'sources'].each do |dir|
         ['one','two'].each do |key|
           FileUtils.mv(Dir.glob(File.join(tmpdir,key,dir,'*')), File.join(tmpdir,'output',dir))
@@ -102,14 +103,14 @@ namespace :bundle do
           end
         end
       end
-      
+
       Dir.glob(File.join(tmpdir,'one','results','*.json')).each do |result_path_one|
         json_one = JSON.parse(File.new(result_path_one).read)
         result_filename = Pathname.new(result_path_one).basename.to_s
         json_two = JSON.parse(File.new(File.join(tmpdir,'two','results',result_filename)).read)
         File.open(File.join(tmpdir,'output','results',result_filename), 'w') {|f| f.write(JSON.pretty_generate(json_one + json_two)) }
       end
-      
+
       json_one = JSON.parse(File.new(File.join(tmpdir,'one','bundle.json')).read)
       json_two = JSON.parse(File.new(File.join(tmpdir,'two','bundle.json')).read)
       json_out = {}
@@ -119,7 +120,7 @@ namespace :bundle do
       ['measures','patients','extensions'].each do |key|
         json_out[key] = (json_one[key] + json_two[key]).uniq
       end
-      
+
       version = json_out['version']
 
       File.open(File.join(tmpdir,'output','bundle.json'), 'w') {|f| f.write(JSON.pretty_generate(json_out)) }
@@ -133,14 +134,14 @@ namespace :bundle do
           zipfile.add(file.sub(path+'/',''),file)
         end
       end
-      
+
       puts "wrote merged bundle to: #{out_zip}"
 
     ensure
       FileUtils.remove_entry_secure tmpdir
     end
-    
-  
+
+
   end
-  
+
 end

data/lib/hqmf-model/population_criteria.rb

@@ -16,7 +16,7 @@ module HQMF
     MSRPOPL = 'MSRPOPL'
     OBSERV = 'OBSERV'
     
-    ALL_POPULATION_CODES = [IPP, DENOM, NUMER, DENEXCEP, DENEX, MSRPOPL, OBSERV]
+    ALL_POPULATION_CODES = [IPP, DENOM, DENEX, NUMER, DENEXCEP, MSRPOPL, OBSERV]
     
     # Create a new population criteria
     # @param [String] id

data/lib/hqmf-parser/1.0/precondition.rb

@@ -28,6 +28,7 @@ module HQMF1
       @preconditions = @entry.xpath('./*/cda:sourceOf[@typeCode="PRCN"]').collect do |entry|
         Precondition.new(entry, self, @doc)
       end
+      check_nil_conjunction_on_child
     end
     
     # Get the conjunction code, e.g. AND, OR

data/lib/hqmf-parser/1.0/restriction.rb

@@ -70,6 +70,8 @@ module HQMF1
         p = Precondition.new(entry, parent, @doc)
         
       end
+
+      check_nil_conjunction_on_child
       
     end
     

data/lib/hqmf-parser/1.0/utilities.rb

@@ -36,6 +36,20 @@ module HQMF1
       end
       clean_json(json)
     end
+
+    # Preconditions can have nil conjunctions as part of a DATEDIFF, we want to remove these and warn
+    def check_nil_conjunction_on_child
+      if (@preconditions.length == 1 && @preconditions.first.conjunction.nil?)
+        bad_precondition = @preconditions.first
+        if (bad_precondition.restrictions.empty? && bad_precondition.subset.nil? && bad_precondition.expression.nil?)
+          @preconditions = @preconditions.first.preconditions
+          puts "\t FIXED PRECONDITION WITHOUT CONJUNCTION"
+        else
+          puts "\t PRECONDITION WITHOUT CONJUNCTION: Cannot be fixed"
+        end
+      end
+    end
+
     
   end
 end  

data/templates/html/_entry.html.erb

@@ -1,6 +1,6 @@
 <tr class="narr_tr">
   
-  <td><%if entry.negationInd %><b>Not Done: </b><% end %><%= entry.description %></td>
+  <td><%if entry.negationInd %><b>Not Done: </b><% end %><%= decode_hqmf_description(entry.description, entry.oid) %></td>
   <td>
     <% entry.codes.each do |set, codes| %>
       <% entry_key = "#{entry.id}_#{by_encounter}" %>

data/templates/html/show.html.erb

@@ -130,9 +130,11 @@
         codes.style.display = 'none';
       }
     </script>
+    <% if measures.length==0 %>
     <div>
       <h3><a href="#" onclick="toggle('table_by_encounter');" id="toggle_button">View By Encounter</a></h3>
     </div>
+    <% end %>
     <%== render :partial => 'entries_by_section', :locals => {patient: patient, code_map: code_map, measures: measures} %>
     <% if measures.length==0 %>
     <%== render :partial => 'entries_by_encounter', :locals => {patient: patient, code_map: code_map, measures: measures} %>

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: health-data-standards
 version: !ruby/object:Gem::Version
-  version: 3.4.3
+  version: 3.4.4
 platform: ruby
 authors:
 - Andy Gregorowicz
@@ -12,7 +12,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-03-06 00:00:00.000000000 Z
+date: 2014-03-25 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rest-client
@@ -175,10 +175,6 @@ executables: []
 extensions: []
 extra_rdoc_files: []
 files:
-- Gemfile
-- README.md
-- Rakefile
-- lib/health-data-standards.rb
 - lib/health-data-standards/export/c32.rb
 - lib/health-data-standards/export/cat_1.rb
 - lib/health-data-standards/export/cat_3.rb
@@ -195,7 +191,6 @@ files:
 - lib/health-data-standards/export/helper/scooped_view_helper.rb
 - lib/health-data-standards/export/html.rb
 - lib/health-data-standards/export/qrda/entry_template_resolver.rb
-- lib/health-data-standards/export/qrda/hqmf-qrda-oids.json
 - lib/health-data-standards/export/rendering_context.rb
 - lib/health-data-standards/export/template_helper.rb
 - lib/health-data-standards/export/view_helper.rb
@@ -330,51 +325,22 @@ files:
 - lib/health-data-standards/models/treating_provider.rb
 - lib/health-data-standards/models/vital_sign.rb
 - lib/health-data-standards/railtie.rb
-- lib/health-data-standards/tasks/bundle.rake
 - lib/health-data-standards/util/code_system_helper.rb
 - lib/health-data-standards/util/hl7_helper.rb
 - lib/health-data-standards/util/hqmf_template_helper.rb
-- lib/health-data-standards/util/hqmf_template_oid_map.json
 - lib/health-data-standards/util/vs_api.rb
-- lib/hqmf-generator/attribute.xml.erb
-- lib/hqmf-generator/characteristic_criteria.xml.erb
-- lib/hqmf-generator/code.xml.erb
-- lib/hqmf-generator/condition_criteria.xml.erb
-- lib/hqmf-generator/derivation.xml.erb
-- lib/hqmf-generator/description.xml.erb
-- lib/hqmf-generator/document.xml.erb
-- lib/hqmf-generator/effective_time.xml.erb
-- lib/hqmf-generator/encounter_criteria.xml.erb
-- lib/hqmf-generator/field.xml.erb
+- lib/health-data-standards.rb
 - lib/hqmf-generator/hqmf-generator.rb
-- lib/hqmf-generator/observation_criteria.xml.erb
-- lib/hqmf-generator/population_criteria.xml.erb
-- lib/hqmf-generator/precondition.xml.erb
-- lib/hqmf-generator/procedure_criteria.xml.erb
-- lib/hqmf-generator/reason.xml.erb
-- lib/hqmf-generator/reference.xml.erb
-- lib/hqmf-generator/source.xml.erb
-- lib/hqmf-generator/specific_occurrence.xml.erb
-- lib/hqmf-generator/subset.xml.erb
-- lib/hqmf-generator/substance_criteria.xml.erb
-- lib/hqmf-generator/supply_criteria.xml.erb
-- lib/hqmf-generator/template_id.xml.erb
-- lib/hqmf-generator/temporal_relationship.xml.erb
-- lib/hqmf-generator/value.xml.erb
-- lib/hqmf-generator/variable_criteria.xml.erb
 - lib/hqmf-model/attribute.rb
-- lib/hqmf-model/data_criteria.json
 - lib/hqmf-model/data_criteria.rb
 - lib/hqmf-model/document.rb
 - lib/hqmf-model/population_criteria.rb
 - lib/hqmf-model/precondition.rb
 - lib/hqmf-model/types.rb
 - lib/hqmf-model/utilities.rb
-- lib/hqmf-parser.rb
 - lib/hqmf-parser/1.0/attribute.rb
 - lib/hqmf-parser/1.0/comparison.rb
 - lib/hqmf-parser/1.0/data_criteria.rb
-- lib/hqmf-parser/1.0/data_criteria_oid_xpath.json
 - lib/hqmf-parser/1.0/document.rb
 - lib/hqmf-parser/1.0/expression.rb
 - lib/hqmf-parser/1.0/observation.rb
@@ -402,6 +368,7 @@ files:
 - lib/hqmf-parser/converter/pass2/comparison_converter.rb
 - lib/hqmf-parser/converter/pass2/operator_converter.rb
 - lib/hqmf-parser/parser.rb
+- lib/hqmf-parser.rb
 - lib/util/counter.rb
 - templates/_author.hdata.erb
 - templates/_pedigree.hdata.erb
@@ -536,6 +503,39 @@ files:
 - templates/html/_section.html.erb
 - templates/html/show.html.erb
 - templates/metadata.hdata.erb
+- lib/health-data-standards/export/qrda/hqmf-qrda-oids.json
+- lib/health-data-standards/util/hqmf_template_oid_map.json
+- lib/hqmf-model/data_criteria.json
+- lib/hqmf-parser/1.0/data_criteria_oid_xpath.json
+- lib/hqmf-generator/attribute.xml.erb
+- lib/hqmf-generator/characteristic_criteria.xml.erb
+- lib/hqmf-generator/code.xml.erb
+- lib/hqmf-generator/condition_criteria.xml.erb
+- lib/hqmf-generator/derivation.xml.erb
+- lib/hqmf-generator/description.xml.erb
+- lib/hqmf-generator/document.xml.erb
+- lib/hqmf-generator/effective_time.xml.erb
+- lib/hqmf-generator/encounter_criteria.xml.erb
+- lib/hqmf-generator/field.xml.erb
+- lib/hqmf-generator/observation_criteria.xml.erb
+- lib/hqmf-generator/population_criteria.xml.erb
+- lib/hqmf-generator/precondition.xml.erb
+- lib/hqmf-generator/procedure_criteria.xml.erb
+- lib/hqmf-generator/reason.xml.erb
+- lib/hqmf-generator/reference.xml.erb
+- lib/hqmf-generator/source.xml.erb
+- lib/hqmf-generator/specific_occurrence.xml.erb
+- lib/hqmf-generator/subset.xml.erb
+- lib/hqmf-generator/substance_criteria.xml.erb
+- lib/hqmf-generator/supply_criteria.xml.erb
+- lib/hqmf-generator/template_id.xml.erb
+- lib/hqmf-generator/temporal_relationship.xml.erb
+- lib/hqmf-generator/value.xml.erb
+- lib/hqmf-generator/variable_criteria.xml.erb
+- lib/health-data-standards/tasks/bundle.rake
+- Gemfile
+- README.md
+- Rakefile
 homepage: https://github.com/projectcypress/health-data-standards
 licenses:
 - APL 2.0
@@ -556,7 +556,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.2.2
+rubygems_version: 2.0.14
 signing_key: 
 specification_version: 4
 summary: A library for generating and consuming various healthcare related formats.